Biology subjects

Hernandez, G. L.

Publications and source records attributed to Hernandez, G. L..

5 recordsLinked to original sources

bioRxiv2026

Multiple approaches for CRISPR-based targeting of DNA methylation to promoters of bacterial and viral susceptibility genes in cassava

Targeted epigenetic modifications of specific gene regulatory regions have the potential to confer beneficial traits for crop improvement. Two recently developed CRISPR/Cas9-based epigenome editing tools were tested in transgenic cassava to target cytosine methylation to the promoter region of MeSWEET10a, a necessary gene for infection by the Cassava bacterial blight pathogen, Xanthomonas phaseoli pv. manihotis. The two systems leverage unique methyltransferases, and each induced distinct DNA methylation profiles at the targeted site, decreased effector-triggered MeSWEET10a expression, and attenuated water-soaking symptoms in inoculated leaves. Further, DNA methylation was simultaneously targeted, in addition to MeSWEET10a, to two susceptibility genes for Cassava brown streak virus. Relative levels of de novo DNA methylation at the three loci were inversely correlated with DNA methylation-antagonizing H3K4me3 marks. Finally, an initial assessment of DNA methylation after one generation indicated specific inheritance of CpG methylation that was unstable in the absence of the methyltransferase systems.

plant biology↗

bioRxiv2025

PlantCV v4: Image analysis software for high-throughput plant phenotyping

PlantCV is an open-source Python project aimed at developing tools to address a range of image-based, plant phenotyping questions. PlantCV has been used for more than 10 years to automate trait collection from image data and the newest release, PlantCV version 4, continues to lower the barrier to entry for users without substantial coding experience through extensive example use-case tutorials and simplified installation. In addition to usability, we document added functionality since the release of PlantCV v2, including support for more image types such as fluorescence, thermal, and hyperspectral data. Finally, we describe the development of a new subpackage focused on morphological trait measurements like leaf angle, and demonstrate its utility as compared to more manual methods of data collection. CORE IDEASO_LIPlantCV is an open-source, open-development, Python-based software package that has a new release for improved functionality and usability to make image analysis flexible and easier for researchers without a coding background. C_LIO_LIPlantCV is now capable of handling new data types that are relevant to researchers, such as thermal and hyperspectral, and has built in functionality for extracting information from these image types. C_LIO_LIThe software project aims to lower the barrier to entry into image analysis for researchers by providing numerous, versioned, interactive tutorials that cover most common use cases, particularly in plant science. C_LI

plant biology↗

bioRxiv2025

Targeting dCas9-SunTag to a susceptibility gene promoter is sufficient for CRISPR interference

Cassava production in sub-Saharan Africa is severely impacted by diseases. Most pathogens require interaction with host susceptibility factors to complete their life cycles and cause disease. Targeted DNA methylation is an epigenetic strategy to alter gene expression in plants and we previously reported that a zinc-finger fused to DMS3 could establish methylation at the promoter of MeSWEET10a, a bacterial susceptibility gene, and this resulted in decreased disease. Here, we attempt a similar strategy for cassava brown streak disease. This disease is caused by the ipomoviruses CBSV and UCBSV. These viruses belong to the family Potyviridae, which has been shown extensively to require host eIF4E-family proteins to infect plants and cause disease. We previously found that cassava plants with simultaneous knockout mutations in two eIF4E genes, nCBP-1 and nCBP-2, resulted in decreased susceptibility to CBSD. Here, we report successful simultaneous targeting of both promoters with methylation using a dCas9-DMRcd-SunTag system. However, in contrast to our previous work with MeSWEET10a, controls indicate that CRISPR interference is occurring in these lines and is sufficient for reduction of gene expression. Future research will use genetic crosses to segregate away the DNA methylation reagents and, if DNA methylation proves heritable, assess whether methylation alone is sufficient increase resistance to CBSD.

plant biology↗

bioRxiv2025

Targeted and random mutagenesis of cassava brown streak disease susceptibility factors reveal molecular determinants of disease severity

Cassava brown streak disease (CBSD) is caused by cassava brown streak viruses (CBSVs) from the family Potyviridae. Potyvirid viral genome-linked protein (VPg) recruitment of host eukaryotic translation initiation factor 4E (eIF4E) proteins is a critical step in the viral life cycle. CBSV VPg interacts with all five cassava eIF4E-family members. Simultaneously knocking out eIF4E-family genes nCBP-1 and nCBP-2, in cultivar 60444, strongly reduces CBSD root symptoms and viral titer but does not result in complete resistance, likely due to gene family redundancy. To test for redundancy, we generated single and double mutants for each clade of the eIF4E gene family in farmer preferred cultivar TME419. Double mutants for the eIF(iso)4E and nCBP clades both exhibited reduced symptom severity, with ncbp-1 ncbp-2 having the strongest phenotype. A yeast two-hybrid screen for nCBP-2 mutants that lose VPg affinity identified fifty-one mutants, including an L51F mutant. This finding is consistent with one of the recovered cassava mutants that had a 6 amino acid deletion, including L51, in nCBP-2 and showed a reduction in symptoms relative to wild type. The data presented here suggest that generating mutations corresponding to L51F of nCBP-2 in multiple or all five cassava eIF4E proteins may lead to stronger resistance to CBSD while avoiding pleiotropic effects.

plant biology↗

bioRxiv2021

Recurring adaptive introgression of a supergene that determines social organization

Introgression has been proposed as an essential source of adaptive genetic variation. However, a key barrier to adaptive introgression is that recombination can break down combinations of alleles that underpin many traits. This barrier might be overcome in supergene regions, where suppressed recombination leads to joint inheritance across many loci. Here, we study the evolution of a large supergene region that determines a major social and ecological trait in Solenopsis fire ants: whether colonies have one queen or multiple queens. Using coalescent-based phylogenies built from the genomes of 365 haploid fire ant males, we show that the supergene variant responsible for multiple-queen colonies evolved in one species and repeatedly spread to other species through introgressive hybridization. This finding highlights how supergene architecture can enable a complex adaptive phenotype to recurrently permeate species boundaries.

evolutionary biology↗